Joining two contigs

It can be relevant to join two contigs for several reasons - e.g. if you:
  1. detect two overlapping contigs using the contig aligner.
  2. have contigs which map to the reference genome and are separated by a gap.
  3. have resequenced regions, made de novo assembly with the resequenced reads included and want to join the new contigs with the existing ones.

It is possible to join two contigs in different ways.

For all join methods described above it is possible to keep the old contigs. This is done by ticking Keep contig under Old contigs, which is useful when joining contigs that represent repetitive elements needed for joining other contigs elsewhere in the mapping.

Note! When joining two contigs, the orientation of the result is not guaranteed to follow the orientation of the original contigs, e.g. two contigs with reverse orientation relative to the reference can result in a contig with forward orientation depending on the join function used. However, the orientation of contigs is usually of no importance and the CLC de novo assemblers will output contigs with a somewhat arbitrary orientation.